Workflow

Click the nodes to obtain details about each step.

Heatmaps

Heatmaps Raw

QC plot

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
File Code 
  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
samplemetadata: "metadata/samples.csv"
classifier_training_data: "refdata/human/classifier_training_data.h5"
reference_gc: refdata/human/reference_gc_grch37.csv

refdir: refdata/
thousand_genomes_snps: refdata/human/thousand_genomes_snps.tsv
ref_genome: refdata/human/GRCh37-lite.fa

mappability:
  local_path: refdata/human/wgEncodeCrgMapabilityAlign50mer.bigWig
  url: http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/release3/wgEncodeCrgMapabilityAlign50mer.bigWig

schnapps:
  mincells: 5
  qualfilter: 0.0

# refdata/human/GRCh37-lite.gc.ws_500000.wig
#refdata/human/GRCh37-lite.map.ws_125_to_500000.wig

hmmcopy:
  bin_size: 200000
  gc_wig_file: hmmcopy_wigfiles/wigfiles/grch37/GRCh37-lite.gc.ws_200000.wig
  map_wig_file: hmmcopy_wigfiles/wigfiles/grch37/GRCh37-lite.map.ws_200000.wig
  ref_genome: refdata/human/GRCh37-lite.fa
  chromosomes:
  - '1'
  - '2'
  - '3'
  - '4'
  - '5'
  - '6'
  - '7'
  - '8'
  - '9'
  - '10'
  - '11'
  - '12'
  - '13'
  - '14'
  - '15'
  - '16'
  - '17'
  - '18'
  - '19'
  - '20'
  - '21'
  - '22'
  - X
  - Y
  docker:
    hmmcopy: hmmcopy:v0.0.6
    single_cell_pipeline: single_cell_pipeline:v0.6.41
  e: 0.999999
  eta: 50000
  exclude_list: refdata/human/repeats.satellite.regions
  g: 3
  good_cells:
  - - median_hmmcopy_reads_per_bin
    - ge
    - 50
  - - is_contaminated
    - in
    - - 'False'
      - 'false'
      - false
  igv_segs_quality_threshold: 0.75
  kappa: "100,100,700,100,25,25,25,25,25,25,25,25"
  lambda: 20
  m: "0,1,2,3,4,5,6,7,8,9,10,11"
  map_cutoff: 0.9
  memory:
    med: 6
  min_mqual: 20
  mu: "0,1,2,3,4,5,6,7,8,9,10,11"
  multipliers: "1,2,3,4,5,6"
  nu: 2.1
  num_states: 12
  s: 1
  smoothing_function: modal
  strength: 1000

infer_haps:
  chromosomes:
  - '1'
  - '2'
  - '3'
  - '4'
  - '5'
  - '6'
  - '7'
  - '8'
  - '9'
  - '10'
  - '11'
  - '12'
  - '13'
  - '14'
  - '15'
  - '16'
  - '17'
  - '18'
  - '19'
  - '20'
  - '21'
  - '22'
  - X
  - Y
  extract_seqdata:
    genome_fai_template: refdata/human/GRCh37-lite.fa.fai
    genome_fasta_template: refdata/human/GRCh37-lite.fa
  max_cores: null
  memory:
    high: 16
    low: 4
    med: 6
  ref_data_dir: refdata/human/

Loading...